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formbio / laava

LAAVA: Long-read AAV Analysis
MIT License
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Nextflow MVP workflow #8

Closed etal closed 6 months ago

etal commented 6 months ago

Nextflow workflow with 2 processes:

  1. Read mapping per the Magdoll/AAV tutorial
  2. Wrapper for the 3 existing scripts.

Tested locally with a small (downsampled) example BAM file and other small test files that are now in the repo under test/. The essential scripts are now under src/, and the Bash scripts used only for Nextflow glue are under bin/.

This workflow version works locally using the (still private) "laava" Docker container within the Nextflow process. It hasn't been tested in the cloud yet.

The name "LAAVA: Long-read AAV Analysis" is now used in these files.

etal commented 6 months ago

This code works for me. OK to merge, @alphabdiallo / @dougnukem / @mcrocker-bioborg ?

alphabdiallo commented 6 months ago

LGMT

alphabdiallo commented 6 months ago

LTGM